The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens

Abstract

The rumen represents the first section of a ruminant animal's stomach, where feed is collected and mixed with microorganisms for initial digestion. The major gas produced in the rumen is CO(2) (65.5 mol%), yet the metabolic characteristics of capnophilic (CO(2)-loving) microorganisms are not well understood. Here we report the 2,314,078 base pair genome sequence of Mannheimia succiniciproducens MBEL55E, a recently isolated capnophilic Gram-negative bacterium from bovine rumen, and analyze its genome contents and metabolic characteristics. The metabolism of M. succiniciproducens was found to be well adapted to the oxygen-free rumen by using fumarate as a major electron acceptor. Genome-scale metabolic flux analysis indicated that CO(2) is important for the carboxylation of phosphoenolpyruvate to oxaloacetate, which is converted to succinic acid by the reductive tricarboxylic acid cycle and menaquinone systems. This characteristic metabolism allows highly efficient production of succinic acid, an important four-carbon industrial chemical.

Mutations in yhiT enable utilization of exogenous pyrimidine intermediates in Salmonella enterica serovar Typhimurium

“…In particular, YhiT possesses conserved domains characteristic of the transporters DcuA and DcuB and shows similarity to DcuB of Bacteroides spp. (54 %) (Kuwahara et al, 2004;Xu et al, 2003), Mannheimia succiniciproducens (53 %) (Hong et al, 2004) and a variety of Campylobacterales (~46 %) (Fouts et al, 2005;Suerbaum et al, 2003), and to DcuA of Photorhabdus luminescens (54 %) (Duchaud et al, 2003) and members of the Campylobacterales (~45 %) (Fouts et al, 2005;Suerbaum et al, 2003;Tomb et al, 1997). Significantly, yhiT harboured the only nucleotide changes observed between the cloned DNA and published sequences, providing strong evidence that the mutant YhiT polypeptides manifest the pyrimidine utilization phenotype.…”

“…(~55 %). Notably, YhiS displays 58 % similarity to AsnB, an L-asparginase II from M. succiniciproducens (Hong et al, 2004) and 41 % similarity to the L-asparginase of A. tumefaciens (Wood et al, 2001).…”

Industrial systems biology

“…These were certainly the highest productivities reported at the time, and were particularly promising given the lignocellulosic feedstock used (mixed substrate glucose and xylose, batch and continuous cultivations were also performed as controls, with similar productivities and yields resulting). In the same year, the 2,314,078 base pair genome sequence of M. succiniciproducens MBEL55E was reported co-currently with the genome-scale reconstructed metabolic network (Hong et al, 2004). The genome-scale reconstructed metabolic network, consisting of 373 reactions (121 reversible and 252 irreversible) and 352 metabolites, predicted, using MFA, a theoretical production of 1.71 and 1.86 mol of succinic acid for every mole of glucose under CO 2 and CO 2 -H 2 atmospheres, respectively (Hong et al, 2004).…”

“…In the same year, the 2,314,078 base pair genome sequence of M. succiniciproducens MBEL55E was reported co-currently with the genome-scale reconstructed metabolic network (Hong et al, 2004). The genome-scale reconstructed metabolic network, consisting of 373 reactions (121 reversible and 252 irreversible) and 352 metabolites, predicted, using MFA, a theoretical production of 1.71 and 1.86 mol of succinic acid for every mole of glucose under CO 2 and CO 2 -H 2 atmospheres, respectively (Hong et al, 2004). As a consequence of the simulations, they note, ''Based on these findings, we now design metabolic engineering strategies for the enhanced production of succinic acid; one such strategy will be increasing the PEP carboxylation flux while decreasing the fluxes to acetic, formic, and lactic acid'' (Hong et al, 2004).…”

“…The genome-scale reconstructed metabolic network, consisting of 373 reactions (121 reversible and 252 irreversible) and 352 metabolites, predicted, using MFA, a theoretical production of 1.71 and 1.86 mol of succinic acid for every mole of glucose under CO 2 and CO 2 -H 2 atmospheres, respectively (Hong et al, 2004). As a consequence of the simulations, they note, ''Based on these findings, we now design metabolic engineering strategies for the enhanced production of succinic acid; one such strategy will be increasing the PEP carboxylation flux while decreasing the fluxes to acetic, formic, and lactic acid'' (Hong et al, 2004). In 2006, the authors constructed a series of knock-out mutants of M. succiniciproducens MBEL55E that included disruption of three CO 2 catalyzing reactions (PEP carboxykinase, PEP carboxylase, malic enzyme) and disruption of four genes responsible for by-product formation of lactate, formate, and acetate (ldhA, pflB, pta, and ackA genes) (Lee et al, 2006a).…”